ProtozoaDB: dynamic visualization and exploration of protozoan genomes

ProtozoaDB (http://www.biowebdb.org/protozoadb) is being developed to initially host both genomics and post-genomics data from Plasmodium falciparum, Entamoeba histolytica, Trypanosoma brucei, T. cruzi and Leishmania major, but will hopefully host other protozoan species as more genomes are sequenced. It is based on the Genomics Unified Schema and offers a modern Web-based interface for user-friendly data visualization and exploration. This database is not intended to duplicate other similar efforts such as GeneDB, PlasmoDB, TcruziDB or even TDRtargets, but to be complementary by providing further analyses with emphasis on distant similarities (HMM-based) and phylogeny-based annotations including orthology analysis. ProtozoaDB will be progressively linked to the above-mentioned databases, focusing in performing a multi-source dynamic combination of information through advanced interoperable Web tools such as Web services. Also, to provide Web services will allow third-party software to retrieve and use data from ProtozoaDB in automated pipelines (workflows) or other interoperable Web technologies, promoting better information reuse and integration. We also expect ProtozoaDB to catalyze the development of local and regional bioinformatics capabilities (research and training), and therefore promote/enhance scientific advancement in developing countries.

[1]  David M. A. Martin,et al.  The Genome of the African Trypanosome Trypanosoma brucei , 2005, Science.

[2]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[3]  B. Haas,et al.  The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease , 2005, Science.

[4]  J. Donelson,et al.  The Genome of the African Trypanosome , 2002 .

[5]  D. Theobald,et al.  Divergent evolution within protein superfolds inferred from profile-based phylogenetics. , 2005, Journal of molecular biology.

[6]  Amit P. Sheth,et al.  Relationship Web: Blazing Semantic Trails between Web Resources , 2007, IEEE Internet Computing.

[7]  Robert D. Finn,et al.  New developments in the InterPro database , 2007, Nucleic Acids Res..

[8]  Narmada Thanki,et al.  CDD: a conserved domain database for interactive domain family analysis , 2006, Nucleic Acids Res..

[9]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[10]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide , 2005, Nucleic Acids Res..

[11]  Jonathan E. Allen,et al.  Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.

[12]  Philippa Rhodes,et al.  ApiDB: integrated resources for the apicomplexan bioinformatics resource center , 2006, Nucleic Acids Res..

[13]  Jessica C. Kissinger,et al.  TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi , 2005, Nucleic Acids Res..

[14]  Heather J Munden,et al.  The Genome of the Kinetoplastid Parasite, Leishmania major , 2005, Science.

[15]  Bernard B. Suh,et al.  The genome of the protist parasite Entamoeba histolytica , 2005, Nature.